So this is the third month I've started to balance my checking account, and the Beginning Balance that comes up never matches my bank statement. The last two months, I just let the system correct the balance. The difference is usually a few hundred dollars or more, so getting concerned about my real balance and what is showing in my register. Also, there is no option to input the correct starting balance.

This may be a silly question. "Why would you worry about your beginning balance?" I think you should be more worried about the Ending Balance being as per your bank statement. The starting balance will be your previously reconciled/balanced amount. You should not normally need to adjust this.